crossing96/oncoscreening huggingface dataset:
Classic bladder exstrophy and adenocarcinoma of the bladder: Methylome analysis provide no evidence for underlying disease-mechanisms of this association.	The bladder exstrophy-epispadias complex (BEEC) represents the severe end of uro-rectal malformation spectrum involving aberrant embryonic morphogenesis of the cloacal membrane and the urorectal septum. The most common form of BEEC is isolated classic bladder exstrophy (CBE). Long-term complications in CBE are malignancies of the bladder with 95% of them being adenocarcinomas. Since CBE and adenocarcinoma of the bladder are rare entities, their frequent co-occurrence suggests a common etiology. Recent studies suggest that promoter methylation of various genes play a crucial role during the phenotypical morphogenesis of adenocarcinomas of urinary bladder. To examine, whether epigenetic processes such as DNA methylation patterns are potentially associated with CBE, we performed Illumina 450 K methylation arrays in blood (n = 10) and tissue samples (n = 2) of CBE patients and healthy matched controls (n = 12). In our analysis, we found total lack of methylation in the blood and methylation differences were restricted to 10 CpG sites in the tissue samples. In comparison to other bladder anomalies, CBE tissue methylation profiles differ from those of adenocarcinoma, adenocarcinoma with CBE, urothelial carcinoma and urachal carcinoma. In this preliminary study, we did not provide any strong evidence of major DNA methylation alterations which would be suggestive for strong underlying epigenetic mechanism. However, larger studies are required to provide more robust statistical evidence to exclude smaller effects in the tissues.	bladder
Association of Smoking and Death from Genitourinary Malignancies: Analysis of the National Longitudinal Mortality Study.	PURPOSE: We explored the association between tobacco use and genitourinary cancer specific survival in a contemporary, nationally representative sample of the United States civilian population. MATERIALS AND METHODS: A total of 493,282 participants in the National Longitudinal Mortality Study who provided detailed tobacco information from 1993 to 2005 were included in study. Our primary outcome was death from bladder, kidney or prostate cancer. Cause of death was determined from death certificates. Analyzed smoking parameters included smoking status at the time of the survey, age at the start of smoking and home smoking rules. Multivariable Cox regression models were used to assess associations of different smoking parameters with bladder, kidney and prostate cancer specific mortality. RESULTS: During a 5-year followup 5.6% of participants who had ever smoked died compared to 3.1% of those who had never smoked (p <0.0001). Of those who died of bladder, kidney and prostate cancer 62%, 58% and 62%, respectively, were ever smokers. On multivariable analysis ever smoking was associated with bladder and kidney cancer mortality (HR 1.92, 95% CI 1.25-2.97, and HR 1.54, 95% CI 1.01-2.34, respectively). Additionally, starting to smoke during teenage years and smoking at home were associated with bladder cancer specific mortality (HR 2.14, 95% CI 1.28-3.56 and HR 2.99, 95% CI 1.34-6.65) and kidney cancer specific mortality (HR 1.65, 95% CI 1.03-2.66 and HR 2.84, 95% CI 1.54-5.23, respectively). However, only everyday smoking was associated with an increased risk of prostate cancer mortality (HR 1.81, 95% CI 1.30-2.53). CONCLUSIONS: In a nationally representative study we confirmed the association between smoking intensity and mortality from genitourinary malignancies. Starting to smoke at a younger age and smoking at home conferred a significantly higher risk of death from bladder and kidney cancers.	bladder
Ag Nanoparticles/α-Ag(2)WO(4) Composite Formed by Electron Beam and Femtosecond Irradiation as Potent Antifungal and Antitumor Agents.	The ability to manipulate the structure and function of promising systems via external stimuli is emerging with the development of reconfigurable and programmable multifunctional materials. Increasing antifungal and antitumor activity requires novel, effective treatments to be diligently sought. In this work, the synthesis, characterization, and in vitro biological screening of pure α-Ag(2)WO(4), irradiated with electrons and with non-focused and focused femtosecond laser beams are reported. We demonstrate, for the first time, that Ag nanoparticles/α-Ag(2)WO(4) composite displays potent antifungal and antitumor activity. This composite had an extreme low inhibition concentration against Candida albicans, cause the modulation of α-Ag(2)WO(4) perform the fungicidal activity more efficient. For tumor activity, it was found that the composite showed a high selectivity against the cancer cells (MB49), thus depleting the populations of cancer cells by necrosis and apoptosis, without the healthy cells (BALB/3T3) being affected.	bladder
Cell block preparation in urine cytology: examination of utility and workflow in an academic practice.	INTRODUCTION: Urine cytology is a common non-invasive test to screen for urothelial carcinoma. Urine cell blocks may sometimes be prepared as a diagnostic aid (eg, to characterize architecture or perform immunohistochemistry). The aim of this study was to determine whether routinely preparing cell blocks on urine specimens improves diagnostic sensitivity. MATERIALS AND METHODS: Three time periods were compared: time period 1 (prior to November 2009; 1437 consecutive selected cases), when cell blocks were rarely prepared; period 2 (November 2009 to May 2010; 1230 selected cases), when cell blocks were prepared on all cases; and period 3 (after May 2010; 1499 consecutive selected cases), when cell blocks were made only when indicated (for samples with substantial cellular pellets or when requested by a pathologist). RESULTS: Patient demographics and the type of specimens received were relatively similar during the 3 time periods. Increased preparation of cell blocks was not accompanied by a notable improvement in specimen adequacy rate, given that <1%, 2%, and 1% of samples were unsatisfactory for the 3 periods. Only the proportion of atypical cases differed during the time periods, being highest in period 1 (23%), but lower in periods 2 and 3. Turnaround time was fastest for period 1 (mean: 47 hours, median: 33 hours), and slower for period 2 and period 3. CONCLUSION: These data show that routinely preparing cell blocks for urine samples did not improve our laboratory's specimen adequacy rate. Nonetheless, cell block preparation on urine samples did help lower the proportion of atypical diagnoses, when routinely or selectively prepared. Because preparation of cell blocks on all urine cases can be costly and only provides minimal added clinical benefit, our recommendation is to rather judiciously utilize cell blocks when screening urine cytology samples.	bladder
DNA methylation patterns in bladder tumors of African American patients point to distinct alterations in xenobiotic metabolism.	Racial/ethnic disparities have a significant impact on bladder cancer outcomes with African American patients demonstrating inferior survival over European-American patients. We hypothesized that epigenetic difference in methylation of tumor DNA is an underlying cause of this survival health disparity. We analyzed bladder tumors from African American and European-American patients using reduced representation bisulfite sequencing (RRBS) to annotate differentially methylated DNA regions. Liquid chromatography-mass spectrometry (LC-MS/MS) based metabolomics and flux studies were performed to examine metabolic pathways that showed significant association to the discovered DNA methylation patterns. RRBS analysis showed frequent hypermethylated CpG islands in African American patients. Further analysis showed that these hypermethylated CpG islands in patients are commonly located in the promoter regions of xenobiotic enzymes that are involved in bladder cancer progression. On follow-up, LC-MS/MS revealed accumulation of glucuronic acid, S-adenosylhomocysteine, and a decrease in S-adenosylmethionine, corroborating findings from the RRBS and mRNA expression analysis indicating increased glucuronidation and methylation capacities in African American patients. Flux analysis experiments with 13C-labeled glucose in cultured African American bladder cancer cells confirmed these findings. Collectively, our studies revealed robust differences in methylation-related metabolism and expression of enzymes regulating xenobiotic metabolism in African American patients indicate that race/ethnic differences in tumor biology may exist in bladder cancer.	bladder
MRI of Tumors and Tumor Mimics in the Female Pelvis: Anatomic Pelvic Space-based Approach.	Pelvic masses can present a diagnostic challenge owing to the difficulty in assessing their origin and the overlap in imaging features. The majority of pelvic tumors arise from gastrointestinal or genitourinary organs, with less common sites of origin including the connective tissues, nerves, and lymphovascular structures. Lesion evaluation usually starts with clinical assessment followed by imaging, or the lesion may be an incidental finding at imaging performed for other clinical indications. Since accurate diagnosis is essential for optimal management, imaging is useful for suggesting the correct diagnosis or narrowing the differential possibilities and distinguishing tumors from their mimics. Some masses may require histologic confirmation of the diagnosis with biopsy and/or up-front surgical resection. In this case, imaging is essential for presurgical planning to assess mass size and location, evaluate the relationship to adjacent pelvic structures, and narrow differential possibilities. Pelvic US is often the first imaging modality performed in women with pelvic symptoms. While US is often useful to detect a pelvic mass, it has significant limitations in assessing masses located deep in the pelvis or near gas-filled organs. CT also has limited value in the pelvis owing to its inferior soft-tissue contrast. MRI is frequently the optimal imaging modality, as it offers both multiplanar capability and excellent soft-tissue contrast. This article highlights the normal anatomy of the pelvic spaces in the female pelvis and focuses on MRI features of common tumors and tumor mimics that arise in these spaces. It provides an interpretative algorithm for approaching an unknown pelvic lesion at MRI. It also discusses surgical management, emphasizing the value of MRI as a road map to surgery and highlighting anatomic locations where surgical resection may present a challenge. (©)RSNA, 2019.	bladder
Kinesin family member C1 accelerates bladder cancer cell proliferation and induces epithelial-mesenchymal transition via Akt/GSK3β signaling.	Kinesin family member C1 (KIFC1) is implicated in the clustering of multiple centrosomes to maintain tumor survival and is thought to be an oncogene in several kinds of cancers. In our experiments, we first performed bioinformatics analysis to investigate the expression levels of KIFC1 in bladder cancer (BC) specimens and normal bladder epitheliums and then, using our samples, verified findings by quantitative real-time PCR and western blotting assays. All data showed that KIFC1 was significantly upregulated in BC specimens at both the mRNA and protein levels. Immunohistochemical studies in a cohort of 152 paraffin-embedded BC tissues displayed that upregulated expression of KIFC1 clearly correlated with pT status (P = .014) and recurrent status (P = .002). Kaplan-Meier survival analysis and log-rank test indicated that patients with BC with high KIFC1 expression had both shorter cancer-specific survival (P < .001) and recurrence-free survival time (P < .001) than those with low KIFC1 expression. Furthermore, ectopic downregulation of KIFC1 weakened BC cell proliferation and migration both in vitro and in vivo, whereas upregulation of KIFC1 enhanced this in vitro. Overexpression of KIFC1 phosphorylated GSK3β and promoted Snail through activating AKT (protein kinase B0) to induce proliferation and epithelial-mesenchymal transition (EMT) and, therefore, substantially promoted BC migration and metastasis. Our study revealed an oncogenic role for KIFC1 to promote BC cell proliferation and EMT via Akt/GSK3β signaling; KIFC1 might be a promising prognostic biomarker as well as a therapeutic target for BC.	bladder
Phase I Trial of an ICAM-1-Targeted Immunotherapeutic-Coxsackievirus A21 (CVA21) as an Oncolytic Agent Against Non Muscle-Invasive Bladder Cancer.	"PURPOSE: The CANON [CAVATAK in NON-muscle-invasive bladder cancer (NMIBC)] study evaluated a novel ICAM-1-targeted immunotherapeutic-coxsackievirus A21 as a novel oncolytic agent against bladder cancer. PATIENTS AND METHODS: Fifteen patients enrolled in this ""window of opportunity"" phase I study, exposing primary bladder cancers to CAVATAK prior to surgery. The first 9 patients received intravesical administration of monotherapy CAVATAK; in the second stage, 6 patients received CAVATAK with a subtherapeutic dose of mitomycin C, known to enhance expression of ICAM-1 on bladder cancer cells. The primary endpoint was to determine patient safety and maximum tolerated dose (MTD). Secondary endpoints were evidence of viral replication, induction of inflammatory cytokines, antitumor activity, and viral-induced changes in resected tissue. RESULTS: Clinical activity of CAVATAK was demonstrated by induction of tumor inflammation and hemorrhage following either single or multiple administrations of CAVATAK in multiple patients, and a complete resolution of tumor in 1 patient. Whether used alone or in combination with mitomycin C, CAVATAK caused marked inflammatory changes within NMIBC tissue biopsies by upregulating IFN-inducible genes, including both immune checkpoint inhibitory genes (PD-L1 and LAG3) and Th1-associated chemokines, as well as the induction of the innate activator RIG-I, compared with bladder cancer tissue from untreated patients. No significant toxicities were reported in any patient, from either virus or combination therapy. CONCLUSIONS: The acceptable safety profile of CAVATAK, proof of viral targeting, replication, and tumor cell death together with the virus-mediated increases in ""immunological heat"" within the tumor microenvironment all indicate that CAVATAK may be potentially considered as a novel therapeutic for NMIBC."	bladder
A rare case of multi-focal human TB after BCG instillation for non-muscle-invasive bladder cancer.	OBJECTIVE: To describe a left epididymitis and para-aortical involvement caused by Mycobacterium tuberculosis hominis reactivation after bacillus Calmette-Guérin instillation for non-muscle-invasive bladder cancer. PATIENT AND METHODS: A Caucasian male, aged 76 years, exposed to bacillus Calmette-Guérin for a high-grade non-muscle-invasive bladder cancer in 2015, reported painful and progressive left scrotal swelling with purulent discharge from a cutaneous fistulous track that yielded, on liquid culture, a pan-susceptible Mycobacterium tuberculosis hominis strain. Moreover, after 6 months of anti-tuberculosis treatment, an abdominal peri-aortic mass, sized 4 cm, was found and a surgical biopsy showed necrotizing granulomas; however, although smear microscopy and Xpert MTB/Rif™ performed on fresh biopsy sample were positive, liquid cultures resulted negative, indicating treatment efficacy. RESULTS: Numerous peculiar and multi-organ involvement due to BCGitis after intravesical immunotherapy have been previously described, including 17 scientific articles about epididymitis, however, no reports so far showed reactivation of Mycobacterium tuberculosis hominis after bacillus Calmette-Guérin treatment. CONCLUSION: Although BCGitis is more prevalent in patients undergoing bacillus Calmette-Guérin instillation for non-muscle-invasive bladder cancer, tuberculosis by other species of Mycobacterium tuberculosis should be always ruled out by molecular and conventional microbiology in patients with a history of Mycobacterium tuberculosis hominis exposure.	bladder
Multicentric analytical comparability study of programmed death-ligand 1 expression on tumor-infiltrating immune cells and tumor cells in urothelial bladder cancer using four clinically developed immunohistochemistry assays.	Programmed death-ligand 1 (PD-L1) expression on tumor cells (TC) or tumor-infiltrating immune cells (IC) correlated in several studies with PD-L1/programmed death-1 (PD-1) checkpoint inhibitor efficacy. Since June 2018, a positive PD-L1 status is required for atezolizumab or pembrolizumab treatment of patients with advanced or metastasized urothelial bladder cancer, who are ineligible for cisplatin-containing therapy. We examined technical comparability and inter-reader agreement of four clinically developed PD-L1 assays in locally advanced disease. Archived, formalin-fixed, paraffin-embedded sections from 30 patients (73.3% cystectomies, 26.7% transurethral resections) were stained by PD-L1 immunohistochemistry using VENTANA SP142, VENTANA SP263, DAKO 22C3, and DAKO 28-8 at two sites per manufacturers' protocols and scored blinded at five sites for PD-L1 expression on IC (% per tumor area) and TC (%). Small, non-significant inter-assay differences were observed for IC. For TC, SP142 showed significantly lower staining percentages. Pairwise comparisons revealed - 0.3 to 1.6% differences in adjusted means between assays for IC, and for TC, - 10.5 to - 7.8% (SP142 versus others) and - 1.9 to 2.7% (other comparisons). Inter-reader and inter-assay agreement was moderate to high for both IC and TC. Allocation to binary cutoffs (1%, 5%, 10%) showed substantial to high Kappa agreement scores (0.440-0.923) for IC and TC between assays for each reader. This first multicenter study, with five independent readers blinded with respect to the assay used, suggests that all four currently clinically relevant assays are analytically similar for evaluation of PD-L1-stained IC and three (SP263, 22C3, and 28-8) for PD-L1-stained TC. Inter-observer agreement for trained readers in scoring of both IC and TC positivity was generally high.	bladder
Amentoflavone Induces Apoptosis and Reduces Expression of Anti-apoptotic and Metastasis-associated Proteins in Bladder Cancer.	BACKGROUND/AIM: Amentoflavone has been shown to be effective against a variety of cancer cells, but its role in bladder cancer remains unclear. Thus, the aim of this study is to evaluate whether amentoflavone may induce toxicity effect of bladder cancer. MATERIALS AND METHODS: Herein, we evaluated amentoflavone effects in a human bladder cancer cell line TSGH8301 in vitro. RESULTS: Amentoflavone caused significant cytotoxicity in TSGH8301 cells at a concentration as low as 200 μM. FAS/FASL-dependent extrinsic apoptosis and mitochondria-dependent intrinsic apoptosis were observed in amentoflavone-treated cells in a dose-dependent manner. Levels of several proapoptotic proteins, such as FAS, FAS-ligand and BAX (B-cell lymphoma 2 associated X) were increased following amentoflavone treatment. Meanwhile, anti-apoptotic MCL-1 (myeloid cell leukemia sequence 1) and cellular FLICE-inhibitory protein (C-FLIP) protein levels were reduced. Additionally, angiogenesis and proliferation-related proteins, including matrix metalloproteinase (MMP)-2, -9, vascular endothelial growth factor (VEGF), urokinase-type plasminogen actvator (uPA) and cyclin D1 were diminished by amentoflavone. CONCLUSION: Amentoflavone induced toxicity of bladder cancer by inhibiting tumor progression and inducing apoptosis signaling transduction.	bladder
Incidence, survival and mortality trends of bladder cancer in Sweden 1997-2016.	Objective: To evaluate trends in bladder cancer incidence, survival and mortality in Sweden from 1997-2016.Patients and methods: The Swedish National Registry of Urinary Bladder Cancer is a nation-wide quality register that started in 1997. It includes information on initial tumor characteristics and treatment; 41,097 new cases were registered up to 2016. Patients were stratified into four time periods. Deaths were monitored through the national death register. Overall and relative survival in time periods were studied with respect to differences in stage, age and gender.Results: The number of new cases increased by 38% for men and 39% for women from 1997 to 2016. The corresponding age-standardized incidence per 100,000 was less dramatic, with increases of 6% and 21%, respectively, and the increase was most evident in the oldest age group. The survival rate was stable until 2012, but thereafter a significant improvement occurred. The survival trends in stage-groups show that this improvement is found in all categories as well as irrespective of age and gender. The mortality rate during this period was stable for women, but showed a slight decrease for men. The main limitation of this study is the use of administrative data for defining some of the endpoints.Conclusion: The most recent Swedish bladder cancer statistics show an increased incidence, improved survival, but stable mortality.	bladder
Radical cystectomy pentafecta: a proposal for standardisation of outcomes reporting following robot-assisted radical cystectomy.	OBJECTIVE: To propose a standardisable composite method for reporting outcomes of radical cystectomy (RC) that incorporates both perioperative morbidity and oncological adequacy. PATIENTS AND METHODS: From July 2010 to December 2017, 277 consecutive patients who underwent robot-assisted RC with intracorporeal urinary diversion (UD) for bladder cancer at our Institution were prospectively analysed. Patients who simultaneously demonstrated negative soft tissue surgical margins (STSMs), ≥16 lymph node (LN) yield, absence of major (grade III-IV) complications at 90 days, absence of UD-related long-term sequelae and absence of clinical recurrence at ≤12 months, were considered as having achieved the RC-pentafecta. A multivariable logistic regression model was assessed to measure predictors for achieving RC-pentafecta. RESULTS AND LIMITATIONS: Since 2010, 270 of 277 patients that had completed at least 12 months of follow-up were included. Over a mean follow-up of 22.3 months, ≥16 LN yield, negative STSMs, absence of major complications at 90 days, and absence of UD-related surgical sequelae and clinical recurrence at ≤12 months were observed in 93.0%, 98.9%, 76.7%, 81.5% and 92.2%, patients, respectively, resulting in a RC-pentafecta rate of 53.3%. Multivariable logistic regression analysis revealed age (odds ratio [OR] 0.95; P = 0.002), type of UD (OR 2.19; P = 0.01) and pN stage (OR 0.48; P = 0.03) as independent predictors for achieving RC-pentafecta. CONCLUSIONS: We present a RC-pentafecta as a standardisable composite endpoint that incorporates perioperative morbidity and oncological adequacy as a potential tool to assess quality of RC. This tool may be useful for assessing the learning curve and calculating cost-effectiveness amongst others but needs to be externally validated in future studies.	bladder